University of Michigan Center for Statistical 
Search Liming's website

woparent.BestRepeat(BestRepeat)R Documentation

Optimal number of repeated measurements for linkage analysis without using parental phenotypes


The program calculates the optimal number of repeated measurements for variance components models for nuclear families when parental phenotypes are not available.


woparent.BestRepeat(Vm, cost.pheno, Va, Vg, Ve, s)


Vm Measurement error variance
cost.pheno Ratio of phenotyping cost to genotyping and subject recruitment cost
Va Major gene effect, the additive genetic variance due to the major gene
Vg Polygenic variance which is the genetic variance due to all residual additive effects not explained by the QTL
Ve Subject-specific environmental variance
s Number of offspring per family


The model assums the total trait variance = Va + Vg + Ve + Vm


The function returns the optimal number of repeated measures.


Wei-Min Chen and Liming Liang


Liang L, Chen WM, Sham PC and Abecasis GR. Variance Components Linkage Analysis with Repeated Measurements (2008)

See Also

BestRepeat, BestRepeat-package


  #Suppose that the genotyping plus recruitment cost per subject is 5 times the phenotyping cost per measure.
  #The measurement error variance is 40.
  #Major gene effect is 20, the polygene effect is 40 and the environmental variance is 40.
  #There are 4 offspring per nuclear family where parental phenotypes are not available.
  #The optimal number of repeated measures is given by

[Package BestRepeat version 1.0 Index]


University of Michigan | School of Public Health